15-55546742-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001367806.1(PYGO1):c.541G>T(p.Ala181Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367806.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYGO1 | NM_001367806.1 | c.541G>T | p.Ala181Ser | missense_variant | Exon 3 of 3 | ENST00000563719.4 | NP_001354735.1 | |
PYGO1 | NM_001330326.2 | c.541G>T | p.Ala181Ser | missense_variant | Exon 3 of 4 | NP_001317255.1 | ||
PYGO1 | NM_015617.3 | c.541G>T | p.Ala181Ser | missense_variant | Exon 3 of 3 | NP_056432.1 | ||
PYGO1 | XM_047432381.1 | c.226G>T | p.Ala76Ser | missense_variant | Exon 3 of 3 | XP_047288337.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYGO1 | ENST00000563719.4 | c.541G>T | p.Ala181Ser | missense_variant | Exon 3 of 3 | 5 | NM_001367806.1 | ENSP00000457777.1 | ||
PYGO1 | ENST00000302000.10 | c.541G>T | p.Ala181Ser | missense_variant | Exon 3 of 3 | 1 | ENSP00000302327.6 | |||
PYGO1 | ENST00000645724.1 | c.541G>T | p.Ala181Ser | missense_variant | Exon 3 of 4 | ENSP00000496139.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251228Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135768
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727210
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.541G>T (p.A181S) alteration is located in exon 3 (coding exon 3) of the PYGO1 gene. This alteration results from a G to T substitution at nucleotide position 541, causing the alanine (A) at amino acid position 181 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at